Assisted model building and energy refinement

The AMBER (Assisted Model Building and Energy Refin emeni) is based on a force field developed for protein and nucleic acid computations by members of the Peter Kollman research group at the... 

P. A. KoUman and co-workers, AMBER Assisted Model Building and Energy Refinement, Urdversity of CaUforrda, San Erancisco, 1980—present ... 

AMBER (Assisted Model Building and Energy Refinement)... 

Alternant hydrocarbon 127 AMBER (Assisted Model Building and Energy Refinement) 45 Angular momentum 155, 296, 304 Anisotropy 284, 293 Antisymmetry 95, 186 Asymmetry parameter 278... 

AMBER Assisted model building and energy refinement. (Ref. 18) Optimized for proteins and DNA. Depend.s on. sy.stem but generally good. 

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

In conjunction with a study on the reactivity of dimeric quinone me-thides, Elder et al. (56) examined the physical and electronic structure of guaiacylglycerol-/ -coniferyl ether, which is substituted in a manner representative of the lignin polymer. Calculations were performed using AMBER (Assisted Model Building with Energy Refinement) (24), which is a force-field method, and the energetic minimum was determined to be a folded structure similar to that reported by Gravitis and Erins (55). 

Weiner, P.K. and Kollman, P.A. (1981) AMBER Assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem. 2, 287-303. 

Tel. 415-476-4637, fax 415-476-0688, e-mail pak cgl.ucsf.edu Assisted Model Building using Energy Refinement. Energy minimization, molecular dynamics, and free energy perturbation (FEP) calculations. SPASMS (San Francisco Package of Applications for the Simulation of Molecular Systems). VAX, Cray versions. 

P. Weiner and P. Kollman, J. Comput. Chem., 2, 287 (1981). AMBER Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions. 

Assisted Model Building with Energy Refinement refers to a MM force field for the simulation of biomolecules and a package of molecular simulation programs. 

Assisted Model Building using Energy Refinement. Energy minimization, molecular dynamics, and free energy perturbation calculations. VAX, Cray, and other versions. 

Wei reported radius- and chirality-dependent conformations of PE on CNT interfaces by MD with the AMBER (assisted model building with energy refinement) force field. ... 

The kind of energy terms, their functional form, and how carefully (number, quality, and kind of reference data) the parameters were derived determine the quality of a force field. Accurate force fields exist for organic molecules (e.g., MM2, MM3), but more approximate force fields (e.g., with fixed bond distances) optimized for computational speed rather than accuracy [e.g., AMBER (assisted model building with energy refinement), CHARMM (chemistry at Harvard molecular mechanics), GROMOS (Groningen molecular simulation)] are the only practical choice for the treatment of large biomolecules. The type of molecular system to be smdied determines the choice of the force field. 

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